/// <summary>
/// Main function to do all the processing.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void ProcessData(string[] args)
{
MTAssembleArguments options = new MTAssembleArguments();
CommandLineArguments parser = new CommandLineArguments();
AddAssembleParameters(parser);
if (args.Length < 1 ||
args[0].Equals("Help", StringComparison.InvariantCultureIgnoreCase) ||
args[0].Equals("/h", StringComparison.CurrentCultureIgnoreCase) ||
args[0].Equals("/help", StringComparison.CurrentCultureIgnoreCase) ||
args[0].Equals("-h", StringComparison.CurrentCultureIgnoreCase) ||
args[0].Equals("-help", StringComparison.CurrentCultureIgnoreCase))
{
//Output.WriteLine(OutputLevel.Required, StaticResources.ASSEMBLE_HELP);
PrintHelp(parser);
}
else
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
//Output.WriteLine(OutputLevel.Required, StaticResources.ASSEMBLE_HELP);
Environment.Exit(-1);
}
if (options.Help)
{
PrintHelp(parser);
}
else
{
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
//TODO: Replace strings in two places with variables in one
var nodeSet = args.Any(z => z.Contains("min_node_count"));
var forceKmer = args.Any(z => z.Contains("force_sqrt"));
if (nodeSet && forceKmer)
{
Console.WriteLine("You cannot set both min_node_count and force_sqrt, as the arguments both alter the same setting.");
return;
}
MTAssembleArguments.MinNodeCountSet = nodeSet;
options.ProcessMTDNA();
}
}
}
/// <summary>
/// Assemble function.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void Assemble(string[] args)
{
MTAssembleArguments options = new MTAssembleArguments();
CommandLineArguments parser = new CommandLineArguments();
AddAssembleParameters(parser);
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
//Output.WriteLine(OutputLevel.Required, StaticResources.ASSEMBLE_HELP);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, StaticResources.ASSEMBLE_HELP);
}
else
{
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
options.AssembleSequences();
}
}
else
{
Output.WriteLine(OutputLevel.Required, StaticResources.ASSEMBLE_HELP);
}
}
